Re: Origin of Life and Temperature

On Jul 9, 7:30 pm, Jeremy.Winfi...@xxxxxxxxx wrote:
I decided to post all my rebuttals in a single email to avoid
spamming.

I.
It's insufficient to say "that's how it's always been" as far as
thinking about the origins of ribosomes, polymerases, tRNAs, ready
made monomers ... the whole works. Although this may seem like an easy
way out (especially without existing precursors), it could've been
possible that Earth was the lucky place in the random universe where
all these elements perfectly aggregated into this complex form. And
even if this is true, some kind of random polymerization must have
taken place, something must have started all this. There is evidence
for non specific polymers spontaneously polymerizing [1, 2]

But, let's check the numbers for a bit. Let's say you want to probe
the complete sequence space for a 200 a.a. polymer (bearing in mind
that most are above 300). Let's try to be practical and only use 15
of the more ancient amino acids. That's 200^15 different proteins,
which is the equivalent of a billion pounds of protein. I just feel
those odds are too great.


I think you mean 15^200 which is enormously larger than 200^15
(15^200 ~ 10^235, 200^15 ~ 10^34).

Inf.

II.
As far as the origin of life occurring around a hydrothermal vent like
a black smoker, I know it seems extremely counter intuitive for life
to occur at 'extremes,' as compared to our room temperature offices.
But, again, it's known that these guys can thrive at 121C.
Thermophiles do exist, so this should cast some doubt on that bias.

The paper previously cited [3] says Planctomycetales are more deeply
rooted. There are some unconsidered factors pointing away from
plactomycetaceae as being closer to the root than thermophiles.
Plactomycetaceae are chemo-organotrophs and obligate aerobes. Since
the predominant compounds in the atmosphere were CO2 and methane, this
casts further doubt on this order being the first around. Also good
to note: Most chemical reactions are known to occur faster at high
temperatures, and many reactions can't occur without metal cofactors.
Since both of these are provided around hydrothermal vents, it seems a
likely place.

I am not convinced that comparing rRNA sequences alone proves their
point. All tree of life papers cite rRNA sequences. It seems, based
on which parts of the sequence you analyze, one can find any bug one
wishes as the origin of life. The nature paper (2002) previously
cited claims only to have used "most conserved positions" of rRNA, but
does not say this is a functionally conserved region, attributing
other changes to the rRNA as "noise." Even if the non conserved
portions of the rRNA are a result of neutral evolution, "noise" is
still a misnomer. Even the paper itself claims this is "inconclusive"
evidence for disproving the ancestry of hyperthermophiles.

A more recent paper (2004, 4) seems to re-establish hyperthermophiles
as being ancient, and use tRNA sequences to back up their conclusions.

The 2002 Nature letter also cites the enzyme gyrase as being
hyperthermophile's recent acquirement from archaea, and indeed,
previous lateral gene transfer has been found in hyperthermophiles.
Indeed, this evidence does not bolster my argument.

I feel a complete picture must take into account tRNA sequences, rRNA
sequences, common proteins, but also protein-protein interactions.
Since no ppi's have been found in thermophiles, we can't say
conclusively which is most closely rooted.

III.
A follow up question for the thymidine dimer adaptation in tRNA's- are
these found in all RNA's? If these are only found in thermophiles,
then it seems to stand reason that it was an ancient adaptation to
help survive in hostile early earth conditions.

Cited:

1. "Self-Assembled Peptide Amphiphile Nanofibers Conjugated to MRI
Contrast Agents." Nano Lett. 2005
2. "Emerging biological materials through molecular self-assembly,"
Biotechnology Advances 2002
3. "A non-hyperthermophilic ancestor for Bacteria," Nature, 2002
4. "The hyperthermophilic orgin of life revisited," Biochem Soc Trans,
2004.



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